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No more use of -D in the integration tests but instead stick with VCFs only. Since all of these tests were duplicated (one each for dbSNP format and for VCF), we don't actually lose coverage in the integration tests.

This commit is contained in:
Eric Banks 2011-08-02 10:39:50 -04:00
parent a2ca994e9a
commit 1c387848de
2 changed files with 2 additions and 21 deletions
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19
public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
View File

@ -32,13 +32,6 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
1,
Arrays.asList(base_md5_with_SW_or_VCF));
executeTest("test realigner defaults with VCF", spec2);
WalkerTestSpec spec3 = new WalkerTestSpec(
baseCommand + "-D " + GATKDataLocation + "dbsnp_129_b36.rod",
1,
Arrays.asList(base_md5));
executeTest("realigner defaults with dbsnp", spec3);
}
@Test
@ -48,12 +41,6 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
1,
Arrays.asList("3dd5d2c9931b375455af0bff1a2c4888"));
executeTest("realigner known indels only from VCF", spec1);
WalkerTestSpec spec2 = new WalkerTestSpec(
baseCommand + "--consensusDeterminationModel KNOWNS_ONLY -D " + GATKDataLocation + "dbsnp_129_b36.rod",
1,
Arrays.asList("05a114623c126b0398fbc1703437461e"));
executeTest("realigner known indels only from dbsnp", spec2);
}
@Test
@ -63,12 +50,6 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
1,
Arrays.asList(base_md5_with_SW_or_VCF));
executeTest("realigner use SW from VCF", spec1);
WalkerTestSpec spec2 = new WalkerTestSpec(
baseCommand + "--consensusDeterminationModel USE_SW -D " + GATKDataLocation + "dbsnp_129_b36.rod",
1,
Arrays.asList(base_md5_with_SW_or_VCF));
executeTest("realigner use SW from dbsnp", spec2);
}
@Test

4
public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java
View File

@ -30,7 +30,7 @@ public class IndelRealignerPerformanceTest extends WalkerTest {
" -LOD 5" +
" -maxConsensuses 100" +
" -greedy 100" +
" -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod" +
" -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
" -o /dev/null" +
" -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" +
" -L chr1:1-5,650,000" +
@ -45,7 +45,7 @@ public class IndelRealignerPerformanceTest extends WalkerTest {
" -LOD 5" +
" -maxConsensuses 100" +
" -greedy 100" +
" -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod" +
" -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.hg18.vcf" +
" -o /dev/null" +
" -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" +
" -L chr1:1-150,000,000" +